DNA 5-Methylcytosine-Specific Amplification and Sequencing

Chang Liu; Xiaolong Cui; Boxuan Simen Zhao; Pradnya Narkhede; Yawei Gao; Jun Liu; Xiaoyang Dou; Qing Dai; Li-Sheng Zhang; Chuan He

doi:10.1021/jacs.9b12707

DNA 5-Methylcytosine-Specific Amplification and Sequencing

J Am Chem Soc. 2020 Mar 11;142(10):4539-4543. doi: 10.1021/jacs.9b12707. Epub 2020 Feb 25.

Authors

Chang Liu^{1

2}, Xiaolong Cui^{1

2}, Boxuan Simen Zhao³, Pradnya Narkhede⁴, Yawei Gao⁵, Jun Liu^{1

2}, Xiaoyang Dou^{1

2}, Qing Dai^{1

2}, Li-Sheng Zhang^{1

2}, Chuan He^{1

2}

Affiliations

¹ Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.
² Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States.
³ Department of Genetics, Stanford University, Stanford, California 94305, United States.
⁴ Department of Chemistry, University of Cambridge, Cambridge CB2 0SP, U.K.
⁵ Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

Abstract

DNA 5-methylcytosine (5mC)-specific mapping has been hampered by severe DNA degradation and the presence of 5-hydroxymethylcytosine (5hmC) using the conventional bisulfite sequencing approach. Here, we present a 5mC-specific whole-genome amplification method (5mC-WGA), with which we achieved 5mC retention during DNA amplification from limited input down to 10 pg scale with limited interference from 5hmC signals, providing DNA 5mC methylome with high reproducibility and accuracy.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

5-Methylcytosine / chemistry*
Animals
DNA / analysis*
DNA / chemistry
DNA Methylation
Humans
Mice
Nucleic Acid Amplification Techniques / methods*
Sequence Analysis, DNA / methods*
Sulfites / chemistry
Whole Genome Sequencing

Substances

Sulfites
5-Methylcytosine
DNA
hydrogen sulfite

Grants and funding

RM1 HG008935/HG/NHGRI NIH HHS/United States